An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona

ABSTRACT In December of 2019, a novel coronavirus, SARS-CoV-2, emerged in the city of Wuhan, China, causing severe morbidity and mortality. Since then, the virus has swept across the globe, causing millions of confirmed infections and hundreds of thousands of deaths. To better understand the nature...

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Autores principales:	Jason T. Ladner, Brendan B. Larsen, Jolene R. Bowers, Crystal M. Hepp, Evan Bolyen, Megan Folkerts, Krystal Sheridan, Ashlyn Pfeiffer, Hayley Yaglom, Darrin Lemmer, Jason W. Sahl, Emily A. Kaelin, Rabia Maqsood, Nicholas A. Bokulich, Grace Quirk, Thomas D. Watts, Kenneth K. Komatsu, Victor Waddell, Efrem S. Lim, J. Gregory Caporaso, David M. Engelthaler, Michael Worobey, Paul Keim
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	Arizona COVID-19 genome analysis molecular clock phylogenetic analysis Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/cc5134e08b3b4432a258f36f9752fc85
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spelling	oai:doaj.org-article:cc5134e08b3b4432a258f36f9752fc852021-11-15T16:19:09ZAn Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona10.1128/mBio.02107-202150-7511https://doaj.org/article/cc5134e08b3b4432a258f36f9752fc852020-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02107-20https://doaj.org/toc/2150-7511ABSTRACT In December of 2019, a novel coronavirus, SARS-CoV-2, emerged in the city of Wuhan, China, causing severe morbidity and mortality. Since then, the virus has swept across the globe, causing millions of confirmed infections and hundreds of thousands of deaths. To better understand the nature of the pandemic and the introduction and spread of the virus in Arizona, we sequenced viral genomes from clinical samples tested at the TGen North Clinical Laboratory, the Arizona Department of Health Services, and those collected as part of community surveillance projects at Arizona State University and the University of Arizona. Phylogenetic analysis of 84 genomes from across Arizona revealed a minimum of 11 distinct introductions inferred to have occurred during February and March. We show that >80% of our sequences descend from strains that were initially circulating widely in Europe but have since dominated the outbreak in the United States. In addition, we show that the first reported case of community transmission in Arizona descended from the Washington state outbreak that was discovered in late February. Notably, none of the observed transmission clusters are epidemiologically linked to the original travel-related case in the state, suggesting successful early isolation and quarantine. Finally, we use molecular clock analyses to demonstrate a lack of identifiable, widespread cryptic transmission in Arizona prior to the middle of February 2020. IMPORTANCE As the COVID-19 pandemic swept across the United States, there was great differential impact on local and regional communities. One of the earliest and hardest hit regions was in New York, while at the same time Arizona (for example) had low incidence. That situation has changed dramatically, with Arizona now having the highest rate of disease increase in the country. Understanding the roots of the pandemic during the initial months is essential as the pandemic continues and reaches new heights. Genomic analysis and phylogenetic modeling of SARS-COV-2 in Arizona can help to reconstruct population composition and predict the earliest undetected introductions. This foundational work represents the basis for future analysis and understanding as the pandemic continues.Jason T. LadnerBrendan B. LarsenJolene R. BowersCrystal M. HeppEvan BolyenMegan FolkertsKrystal SheridanAshlyn PfeifferHayley YaglomDarrin LemmerJason W. SahlEmily A. KaelinRabia MaqsoodNicholas A. BokulichGrace QuirkThomas D. WattsKenneth K. KomatsuVictor WaddellEfrem S. LimJ. Gregory CaporasoDavid M. EngelthalerMichael WorobeyPaul KeimAmerican Society for MicrobiologyarticleArizonaCOVID-19genome analysismolecular clockphylogenetic analysisMicrobiologyQR1-502ENmBio, Vol 11, Iss 5 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Arizona COVID-19 genome analysis molecular clock phylogenetic analysis Microbiology QR1-502
spellingShingle	Arizona COVID-19 genome analysis molecular clock phylogenetic analysis Microbiology QR1-502 Jason T. Ladner Brendan B. Larsen Jolene R. Bowers Crystal M. Hepp Evan Bolyen Megan Folkerts Krystal Sheridan Ashlyn Pfeiffer Hayley Yaglom Darrin Lemmer Jason W. Sahl Emily A. Kaelin Rabia Maqsood Nicholas A. Bokulich Grace Quirk Thomas D. Watts Kenneth K. Komatsu Victor Waddell Efrem S. Lim J. Gregory Caporaso David M. Engelthaler Michael Worobey Paul Keim An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona
description	ABSTRACT In December of 2019, a novel coronavirus, SARS-CoV-2, emerged in the city of Wuhan, China, causing severe morbidity and mortality. Since then, the virus has swept across the globe, causing millions of confirmed infections and hundreds of thousands of deaths. To better understand the nature of the pandemic and the introduction and spread of the virus in Arizona, we sequenced viral genomes from clinical samples tested at the TGen North Clinical Laboratory, the Arizona Department of Health Services, and those collected as part of community surveillance projects at Arizona State University and the University of Arizona. Phylogenetic analysis of 84 genomes from across Arizona revealed a minimum of 11 distinct introductions inferred to have occurred during February and March. We show that >80% of our sequences descend from strains that were initially circulating widely in Europe but have since dominated the outbreak in the United States. In addition, we show that the first reported case of community transmission in Arizona descended from the Washington state outbreak that was discovered in late February. Notably, none of the observed transmission clusters are epidemiologically linked to the original travel-related case in the state, suggesting successful early isolation and quarantine. Finally, we use molecular clock analyses to demonstrate a lack of identifiable, widespread cryptic transmission in Arizona prior to the middle of February 2020. IMPORTANCE As the COVID-19 pandemic swept across the United States, there was great differential impact on local and regional communities. One of the earliest and hardest hit regions was in New York, while at the same time Arizona (for example) had low incidence. That situation has changed dramatically, with Arizona now having the highest rate of disease increase in the country. Understanding the roots of the pandemic during the initial months is essential as the pandemic continues and reaches new heights. Genomic analysis and phylogenetic modeling of SARS-COV-2 in Arizona can help to reconstruct population composition and predict the earliest undetected introductions. This foundational work represents the basis for future analysis and understanding as the pandemic continues.
format	article
author	Jason T. Ladner Brendan B. Larsen Jolene R. Bowers Crystal M. Hepp Evan Bolyen Megan Folkerts Krystal Sheridan Ashlyn Pfeiffer Hayley Yaglom Darrin Lemmer Jason W. Sahl Emily A. Kaelin Rabia Maqsood Nicholas A. Bokulich Grace Quirk Thomas D. Watts Kenneth K. Komatsu Victor Waddell Efrem S. Lim J. Gregory Caporaso David M. Engelthaler Michael Worobey Paul Keim
author_facet	Jason T. Ladner Brendan B. Larsen Jolene R. Bowers Crystal M. Hepp Evan Bolyen Megan Folkerts Krystal Sheridan Ashlyn Pfeiffer Hayley Yaglom Darrin Lemmer Jason W. Sahl Emily A. Kaelin Rabia Maqsood Nicholas A. Bokulich Grace Quirk Thomas D. Watts Kenneth K. Komatsu Victor Waddell Efrem S. Lim J. Gregory Caporaso David M. Engelthaler Michael Worobey Paul Keim
author_sort	Jason T. Ladner
title	An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona
title_short	An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona
title_full	An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona
title_fullStr	An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona
title_full_unstemmed	An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona
title_sort	early pandemic analysis of sars-cov-2 population structure and dynamics in arizona
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/cc5134e08b3b4432a258f36f9752fc85
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An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona

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